[R] inconsistency in mclapply.....

[Eric Berger]

Hi Akshay,
You do not have to quit R to run 'top'. You can have, for example, 2
windows, with R running in one and top running in the oher.

Eric

On Sat, Jun 10, 2023 at 12:19 AM akshay kulkarni <akshay_e4 using hotmail.com>
wrote:

> Dear Ivan,
>                   Thanks for the reply. I am pressurised by a fast
> approaching deadline and your reply calmed me...
>
> Take a look at the following code:
>
>
> debug at <tmp>#26: LYG <- mclapply(LYGH, FUN = arfima, mc.cores = 2,
> mc.preschedule = FALSE)
> Browse[2]> length(LYGH)
> [1] 357
> Browse[2]>
> ^C
>
> Browse[2]> LYG <- pbmclapply(LYGH,FUN = arfima,mc.cores = 2,mc.preschedule
> = FALSE)
>   |
>
>  |   0%, ETA NA
>
> I am debuuging a function FUN wherein the above expressions appear. The
> pbmclapply code works well if called inside FUN:
> > FUN(arg)
> Result..
>
> But as you may note, it doesn't work while in debug mode....
>
> Also, if I replace pbmclapply by maclapply inside FUN, it hangs....
>
> You might be interested in this:
>
> [ec2-user using ip-172-31-15-116 ~]$ exit
> logout
> There are stopped jobs.
>
> THis occurs when I close R and try to exit the shell prompt( I am on an
> AWS EC2 RHEL 8 Instance). Can this lead you somewhere? As of now I have
> quit R in my machine, so I can't get session info..but please let me know
> if you need it necessarily...
>
> by the by, how do you run top when running R? I think at least in my
> machine, you have to quit R to get to the shell prompt...
>
> I request you TO PLEASE reply to this mail as early as possible. I am
> facing an imminent deadline...please excuse my blatant violation of
> protocol, but deadlines are deadlines, right?
>
> THanking you,
> Yours sincerely,
> AKSHAY M KULKARNI
>
>
> ________________________________
> From: Ivan Krylov <krylov.r00t using gmail.com>
> Sent: Saturday, June 10, 2023 1:43 AM
> To: akshay kulkarni <akshay_e4 using hotmail.com>
> Cc: R help Mailing list <r-help using r-project.org>
> Subject: Re: [R] inconsistency in mclapply.....
>
> On Fri, 9 Jun 2023 18:01:44 +0000
> akshay kulkarni <akshay_e4 using hotmail.com> wrote:
>
> > > LYG <- pbmclapply(LYGH,FUN = arfima,mc.cores = 2,mc.preschedule =
> > > FALSE)
> >   |
> >
>          |
> >   0%, ETA NA^
> >
> > It just hangs.
>
> My questions from the last time still stand:
>
> 0) What is your sessionInfo()? Maybe you're running a parallel BLAS
> which doesn't always handle fork() or something. It may be worth
> disabling BLAS-level parallelism as long as you're already trying to
> use 100% of your processor by other means.
>
> 1) What does traceback() show after you interrupt pbmclapply? Most
> likely, you would be interrupting selectChildren(), but if not, the
> problem may lie in a very different place from what I'm expecting.
>
> 2) While pbmclapply is hung, without interrupting it, take a look at
> the state of the system and the processes on it (are you still on RHEL?
> use `top` or whatever task manager you're comfortable with).
>
>  a) Is 100% of the CPU being used? 100% of one core? Is system mostly
>  idle?
>
>  b) Can you find the child processes launched by pbmclapply?
>
>  c) Write down the PID of the child process and attach a debugger to
>  it (If you're on RHEL, try following this guide:
>  <https://beej.us/guide/bggdb/#attach>. If GDB asks you to install
>  additional debug symbols by running debuginfo-install, follow its
>  guidance and then restart GDB.) and obtain a backtrace. (In GDB, the
>  command to obtain a backtrace is "backtrace".) Which function is the
>  child process stuck in?
>
> --
> Best regards,
> Ivan
>
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>
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